149 research outputs found
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case
Classifications and phylogenetic inferences of organismal groups change in
light of new insights. Over time these changes can result in an imperfect
tracking of taxonomic perspectives through the re-/use of Code-compliant or
informal names. To mitigate these limitations, we introduce a novel approach
for aligning taxonomies through the interaction of human experts and logic
reasoners. We explore the performance of this approach with the Perelleschus
use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies
published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of
names individuated according to their respective source publications), and 75
expert-asserted Region Connection Calculus articulations (e.g., congruence,
proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is
used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous
constraints and interpretations. The reasoning workflow optimizes the logical
consistency and expressiveness of the input and infers the set of maximally
informative relations among the entailed taxonomic concepts. The latter are
then used to produce merge visualizations that represent all congruent and
non-congruent taxonomic elements among the aligned input trees. In this small
use case with 6-53 input concepts per alignment, the information gained through
the reasoning process is on average one order of magnitude greater than in the
input. The approach offers scalable solutions for tracking provenance among
succeeding taxonomic perspectives that may have differential biases in naming
conventions, phylogenetic resolution, ingroup and outgroup sampling, or
ostensive (member-referencing) versus intensional (property-referencing)
concepts and articulations.Comment: 30 pages, 16 figure
Dating the Cryptococcus gattii Dispersal to the North American Pacific Northwest.
The emergence of Cryptococcus gattii, previously regarded as a predominantly tropical pathogen, in the temperate climate of the North American Pacific Northwest (PNW) in 1999 prompted several questions. The most prevalent among these was the timing of the introduction of this pathogen to this novel environment. Here, we infer tip-dated timing estimates for the three clonal C. gattii populations observed in the PNW, VGIIa, VGIIb, and VGIIc, based on whole-genome sequencing of 134 C. gattii isolates and using Bayesian evolutionary analysis by sampling trees (BEAST). We estimated the nucleotide substitution rate for each lineage (1.59 Ă 10-8, 1.59 Ă 10-8, and 2.70 Ă 10-8, respectively) to be an order of magnitude higher than common neutral fungal mutation rates (2.0 Ă 10-9), indicating a microevolutionary rate (e.g., successive clonal generations in a laboratory) in comparison to a species' slower, macroevolutionary rate (e.g., when using fossil records). The clonal nature of the PNW C. gattii emergence over a narrow number of years would therefore possibly explain our higher mutation rates. Our results suggest that the mean time to most recent common ancestor for all three sublineages occurred within the last 60 to 100 years. While the cause of C. gattii dispersal to the PNW is still unclear, our research estimates that the arrival is neither ancient nor very recent (i.e., <25 years ago), making a strong case for an anthropogenic introduction. IMPORTANCE The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events
Golden Trail: Retrieving the Data History that Matters from a Comprehensive Provenance Repository
Experimental science can be thought of as the exploration of a large research space, in search of a few valuable results. While it is this âGolden Dataâ that gets published, the history of the exploration is often as valuable to the scientists as some of its outcomes. We envision an e-research infrastructure that is capable of systematically and automatically recording such history â an assumption that holds today for a number of workflow management systems routinely used in e-science. In keeping with our gold rush metaphor, the provenance of a valuable result is a âGolden Trailâ. Logically, this represents a detailed account of how the Golden Data was arrived at, and technically it is a sub-graph in the much larger graph of provenance traces that collectively tell the story of the entire research (or of some of it).In this paper we describe a model and architecture for a repository dedicated to storing provenance traces and selectively retrieving Golden Trails from it. As traces from multiple experiments over long periods of time are accommodated, the trails may be sub-graphs of one trace, or they may be the logical representation of a virtual experiment obtained by joining together traces that share common data.The project has been carried out within the Provenance Working Group of the Data Observation Network for Earth (DataONE) NSF project. Ultimately, our longer-term plan is to integrate the provenance repository into the data preservation architecture currently being developed by DataONE
The First Provenance Challenge
The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions
The Grizzly, January 28, 1991
Policies and Statistics, A Security Concern: New Quad Regulations; Crime Report Released âą Sonia Sanchez: Poet for Peace âą Gulf Dialogue Continues âą Independence Dogs âą Financial Aid Month âą You Asked for it: You Got It!! âą New Quad Policy âą Presidency Symposium âą When is Dr. Martin Luther King, Jr.\u27s Birthday? âą Who\u27s Who Announced âą Mission Conference Held âą Back to the Basics âą The Innocent âą Swimmers on Win Streak âą Women Hope for Good Things to Come âą A Roller Coaster Season for the Hoopsters âą Women Rounding-out Season âą The Dream Lives On âą Letter: Bundle Up! âą Researchers Psyched Out âą The Technology of War âą A Wasted Solution?https://digitalcommons.ursinus.edu/grizzlynews/1268/thumbnail.jp
Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers
The James Webb Space Telescope Mission
Twenty-six years ago a small committee report, building on earlier studies,
expounded a compelling and poetic vision for the future of astronomy, calling
for an infrared-optimized space telescope with an aperture of at least .
With the support of their governments in the US, Europe, and Canada, 20,000
people realized that vision as the James Webb Space Telescope. A
generation of astronomers will celebrate their accomplishments for the life of
the mission, potentially as long as 20 years, and beyond. This report and the
scientific discoveries that follow are extended thank-you notes to the 20,000
team members. The telescope is working perfectly, with much better image
quality than expected. In this and accompanying papers, we give a brief
history, describe the observatory, outline its objectives and current observing
program, and discuss the inventions and people who made it possible. We cite
detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space
Telescope Overview, 29 pages, 4 figure
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